Apps like 'Synaptic' and 'Root Terminal' when launched from a desktop menu (e.g., your panel's applications menu) will ask for authentication. By default, Debian uses gksu for these tasks. However, it's possible and quite easy to configure things so gksudo is used instead. The following assumes you have already configured your system and user to use sudo.
I first learned how to do change the setting by using gconf-editor. If you have gconf-editor installed, go to the entry for /apps/gksu and click the checkbox next to sudo-mode. But that's the fiddly way to do it. I just discovered by accident a much easier way -- one that doesn't require gconf-editor. Simply launch:
as user (not root) and set Authentication mode to su (to use gksu) or sudo (for gksudo). While you're there, you can also disable screen grabbing, though why you'd want to I'm not really sure.
Note that this is a per user setting. There's probably a system-wide config for this, but I'm feeling too lazy to find it.